TypeError: 'map' object is not subscriptable #47
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HI,
Sorry about the issue. What version of seqcluster are you running?
If I can have the input files I can try to debug. If it is not possible to
share the files, I usually add a pdb.trace_back() with a try/except
statement to get control of the exact point the issue is happening, and
then look at the exact variable is having the issue.
Let me know if you can share with me your files.
Cheers
On July 24, 2019 at 3:30:48 AM, Luohao Xu (notifications@github.com) wrote:
Hi, I came across this error
TypeError: 'map' object is not subscriptable
INFO 1834545 Clusters read
INFO Creating meta-clusters based on shared sequences: 61291
99% (61244 of 61291) |################# | Elapsed Time: 7:19:39 ETA:
0:00:00INFO 512 metaclusters from 33960 sequences
INFO 512 clusters found
INFO counts after: 19759492
INFO # sequences after: 61375
INFO Solving multi-mapping events in the network of clusters
INFO Number of loci: 1834545
N/A% (0 of 512) | | Elapsed Time: 0:00:00 ETA: --:--:--Traceback (most
recent call last):
File "/scratch/luohao/software/seqcluster/bin/seqcluster", line 10, in
sys.exit(main())
File
"/scratch/luohao/software/seqcluster/lib/python3.6/site-packages/seqcluster/command_line.py",
line 28, in main
cluster(kwargs["args"])
File
"/scratch/luohao/software/seqcluster/lib/python3.6/site-packages/seqcluster/make_clusters.py",
line 76, in cluster
clusLred = _cleaning(clusL, args.dir_out)
File
"/scratch/luohao/software/seqcluster/lib/python3.6/site-packages/seqcluster/make_clusters.py",
line 294, in _cleaning
clus_obj = reduceloci(clusL, path)
File
"/scratch/luohao/software/seqcluster/lib/python3.6/site-packages/seqcluster/detect/metacluster.py",
line 77, in reduceloci
_write_cluster(c, clus_obj.clus, clus_obj.loci, n_cluster, path)
File
"/scratch/luohao/software/seqcluster/lib/python3.6/site-packages/seqcluster/detect/metacluster.py",
line 102, in _write_cluster
print("\t".join(pos[:4] + [str(len(cluster[idc].loci2seq[idl]))] +
[pos[-1]]), file=out_handle, end="")
TypeError: 'map' object is not subscriptable
100% (61291 of 61291) |##################| Elapsed Time: 7:20:41 Time:
7:20:41
100% (512 of 512) |######################| Elapsed Time: 0:00:14 Time:
0:00:14
Thanks,
Luohao
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Hi,
I installed it via conda, the version should be 1.2.5
https://drive.google.com/drive/folders/1ck16RgzuG9J5gl8GyHRU_ZH17WwqMaKx?usp=sharing
(please request for access if not accessible)
On Wed, Jul 24, 2019 at 3:09 PM Lorena Pantano <notifications@github.com>
wrote:
… HI,
Sorry about the issue. What version of seqcluster are you running?
If I can have the input files I can try to debug. If it is not possible to
share the files, I usually add a pdb.trace_back() with a try/except
statement to get control of the exact point the issue is happening, and
then look at the exact variable is having the issue.
Let me know if you can share with me your files.
Cheers
On July 24, 2019 at 3:30:48 AM, Luohao Xu ***@***.***)
wrote:
Hi, I came across this error
TypeError: 'map' object is not subscriptable
INFO 1834545 Clusters read
INFO Creating meta-clusters based on shared sequences: 61291
99% (61244 of 61291) |################# | Elapsed Time: 7:19:39 ETA:
0:00:00INFO 512 metaclusters from 33960 sequences
INFO 512 clusters found
INFO counts after: 19759492
INFO # sequences after: 61375
INFO Solving multi-mapping events in the network of clusters
INFO Number of loci: 1834545
N/A% (0 of 512) | | Elapsed Time: 0:00:00 ETA: --:--:--Traceback (most
recent call last):
File "/scratch/luohao/software/seqcluster/bin/seqcluster", line 10, in
sys.exit(main())
File
"/scratch/luohao/software/seqcluster/lib/python3.6/site-packages/seqcluster/command_line.py",
line 28, in main
cluster(kwargs["args"])
File
"/scratch/luohao/software/seqcluster/lib/python3.6/site-packages/seqcluster/make_clusters.py",
line 76, in cluster
clusLred = _cleaning(clusL, args.dir_out)
File
"/scratch/luohao/software/seqcluster/lib/python3.6/site-packages/seqcluster/make_clusters.py",
line 294, in _cleaning
clus_obj = reduceloci(clusL, path)
File
"/scratch/luohao/software/seqcluster/lib/python3.6/site-packages/seqcluster/detect/metacluster.py",
line 77, in reduceloci
_write_cluster(c, clus_obj.clus, clus_obj.loci, n_cluster, path)
File
"/scratch/luohao/software/seqcluster/lib/python3.6/site-packages/seqcluster/detect/metacluster.py",
line 102, in _write_cluster
print("\t".join(pos[:4] + [str(len(cluster[idc].loci2seq[idl]))] +
[pos[-1]]), file=out_handle, end="")
TypeError: 'map' object is not subscriptable
100% (61291 of 61291) |##################| Elapsed Time: 7:20:41 Time:
7:20:41
100% (512 of 512) |######################| Elapsed Time: 0:00:14 Time:
0:00:14
Thanks,
Luohao
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thank you, I am working on this issue, although I see for the numbers that the sequences sparsed a lot over the genome and there are a big number of loci compared to sequences. That normally indicates is not a typical small RNA data. Can I know what kit was used to produce this data, or the size distribution of the reads? is there a peak at any size? Due to this, the debugging time can be larger because it is taking a lot of time to go through all those loci. But I will try to find the issue. Thank you |
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Hi,
I am re-analyzing the data from
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4855716/
The data should be fine. Maybe rRNAs and tRNAs need to be filtered first?
L
…On Fri, Jul 26, 2019 at 8:00 PM Lorena Pantano ***@***.***> wrote:
thank you, I am working on this issue, although I see for the numbers that
the sequences sparsed a lot over the genome and there are a big number of
loci compared to sequences. That normally indicates is not a typical small
RNA data.
Can I know what kit was used to produce this data, or the size
distribution of the reads? is there a peak at any size?
Due to this, the debugging time can be larger because it is taking a lot
of time to go through all those loci. But I will try to find the issue.
Thank you
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Thanks for the link.
Meanwhile I am debugging this, do you think you can try to remove the
scaffold before mapping and reduce -m option to 100-200. Just want to check
if that makes the data less duplicative.
Thanks
|
|
Please find the file 'seqs.m100.sort.bam' in the same drive folder.
…On Fri, Jul 26, 2019 at 9:16 PM Lorena Pantano ***@***.***> wrote:
Thanks for the link.
Meanwhile I am debugging this, do you think you can try to remove the
scaffold before mapping and reduce -m option to 100-200. Just want to check
if that makes the data less duplicative.
Thanks
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Hi, did you try to run that file to see if it breaks as well. It is working with that file for me, just want to confirm is not a user-specific error. Thanks |
lpantano
added a commit
that referenced
this issue
Sep 20, 2019
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This is now fixed, version 1.2.7 should work now. |
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Hi, I came across this error
TypeError: 'map' object is not subscriptable
Thanks,
Luohao
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